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ANATOMIX SOLEIL Synchrotron

The beamline ANATOMIX (Advanced Nanotomography and Imaging with coherent X rays) works at photon energies between 5 and 50 keV. It is dedicated to full-field radiography and tomography in absorption and phase contrast, with pixel sizes from 20 nm to 20 µm.

Three images showing photographs of the microtomograph (left), a 3D volume rendering of a lizard head (center) and the transmission X-ray microscope (right)

Covid-19 consequences on ANATOMIX:Logo du programme Investissements d'Avenir

  • All experiments until end April 2020 are postponed to a later date.
  • The beamline team remains at your disposal (e-mail, see "Contacts" below) for all matters.

(Last updated 3 April 2020)

ANATOMIX, an Equipment of Excellence

Construction and operation of the beamline are largely funded by the French State through the project NanoimagesX in the EQUIPEX program within the framework "Investissements d'avenir" of the French National Research Agency (ANR).

About ANATOMIX

Photo of the extension building housing beamlines ANATOMIX and NANOSCOPIUMANATOMIX is a beamline for X-ray tomography on the micro- and nanoscale, in absorption and phase contrast. It operates in the energy range from 5 keV upward and allows its users to obtain two- and three-dimensional radiographic images of bulk volume samples of macroscopic size (up to several cm thickness). For smaller samples, spatial resolution down to 80 nm (20 nm pixel size) is available. Real-time studies are possible at speeds of up to one microtomography scan per second; higher speeds are envisioned.

A sample interface designed to be as flexible as possible enables in situ and/or in operando studies under conditions similar to the natural or working environment of the samples (temperature, humidity, mechanical load, transport processes). Biological samples can be measured without dehydration and, in many cases, without chemical fixation.

 

Experimental techniques on ANATOMIX

Two classes of radiographic methods are available: parallel-beam microimaging and transmission X-ray microscopy.

Schematic of parallel-beam microtomography Schematic of transmission X-ray microscopy
  • Photon energies from 10 to 50 keV
    (up to approx. 25 keV with monochromatic beam)
  • Beam size up to 40 mm width
  • Resolution down to approx. 1 µm (pixel size 0.3 µm)
  • Absorption contrast (operational)
  • Inline phase contrast (operational)
  • X-ray grating interferometry (planned)
  • Photon energy 10 keV: operational (AP24)
  • Other photon energies from 5 to 20 keV under test
  • X-ray image magnification via zone-plate X-ray lenses
  • Resolution down to approx. 80 nm (pixel size 20 nm)
  • Field of view ≈ (40 µm)2
  • Absorption contrast
  • Zernike phase contrast
Examples: Parallel-beam microtomography
Grayscale image of a virtual cut through the head of a lizard[+] Microtomography with a wide beam: Tomographic slice through the head of a common wall lizard (Podarcis muralis). Note the soft tissue details, visible through X-ray phase contrast. The dead animal was kept in ethanol for the measurements. Data acquired on ANATOMIX using an indirect detector (scintillator LuAG, 1× photo-objective optics and a scientific CMOS camera) with an effective pixel size of 6.5 µm, resulting in a spatial resolution around 15 µm. The volume data set was collected in 7 minutes using a filtered white X-ray beam with a central energy around 25 keV, at a sample–detector distance of 1.2 m.
Horizontal X-ray phase-contrast microtomography slice through the kidney of a mouse[+] Tomography of stained soft tissue: Horizontal X-ray phase-contrast microtomography slice through the kidney of a mouse. The full volume was recorded in 5 minutes at 17 keV and a sample–detector distance of 33 mm, using an indirect detector (scintillator, 5× microscope objective and a scientific CMOS camera) with an effective pixel size of 1.3 µm, resulting in a spatial resolution around 2.5 µm. Phase retrieval by Paganin filtering was applied to obtain the images shown. The specimen was prepared using 90 mg/ml iodine contrast agent in 2% agar. Left: full slice. Right: enlarged detail of the left image. Sample courtesy Georg Schulz, Biomaterials Science Center, University of Basel, Switzerland.
Microtomography slice through a piece of shale rock with foraminifera inclusions, acquired with a pixel size of 0.65 µm - beamline ANATOMIX[+] Extended-field microtomography: Vertical tomography slice through a piece of shale rock with foraminifera inclusions, acquired with a pixel size of 0.65 µm. The field of view was extended by positioning the rotation axis away from the center of the detector field of view. Sample courtesy R. Pellenq, MSE², umi.mit.edu, Massachusetts Institute of Technology / CNRS / Aix-Marseille Université, Cambridge, Massachusetts, USA.
Examples: Transmission X-ray microscopy
Nanotomography slice of a sample of cement paste - beamline ANATOMIX[+] Nanotomography slice of a sample of cement paste at 10 keV. The TXM was used in Zernike phase contrast at a pixel size of 21 nm. The estimated resolution is 85 nm (H) × 75 nm (V). The sample cylinder was prepared with FIB-SEM (i.e., focused-ion-beam milling combined with scanning electron microscopy). Sample courtesy R. Pellenq, MSE², umi.mit.edu, Massachusetts Institute of Technology / CNRS / Aix-Marseille Université, Cambridge, Massachusetts, USA.
Local TXM nanotomography of mouse pancreas - beamline ANATOMIX[+] Local nanotomography of soft biological tissue, here: a murine pancreas at 10 keV. The image shows an axial slice through the reconstructed volume. The TXM was used in Zernike phase contrast at a pixel size of 44 nm. The estimated resolution is about 200 nm. The total exposure time for the scan was 133 minutes. The pancreas was extracted, fixed in formol, then dehydrated and included in paraffin. The sample was cut into a cube column of 1.5 mm diameter and a volume of 40 µm diameter and 40 µm height was imaged in local tomography. Sample courtesy Raphael Scharfmann, INSERM / Institut Cochin, Paris, France.

See also

 

Contacts

Want to perform an experiment on ANATOMIX? Or find out whether the beamline might be suited for your project? The ANATOMIX beamline scientists are happy to answer your questions and give advice:

Timm Weitkamp +33 (0)1 69 35 81 37
timm.weitkamp@synchrotron-soleil.fr
Mario Scheel +33 (0)1 69 35 96 31
mario.scheel@synchrotron-soleil.fr
Jonathan Perrin +33 (0)1 69 35 94 99
jonathan.perrin@synchrotron-soleil.fr

Telephone numbers of beamline rooms

Beamline control room near optics hutches +33 (0)1 69 35 97 31
Beamline control room experiments
Experiment hutch EH3 +33 (0)1 69 35 97 82
Experiment hutch EH4
Meeting and data analysis room +33 (0)1 69 35 97 71
Preparation laboratory
Workshop +33 (0)1 69 35 99 80

Team

DANIEL
DANIEL Guillaume
Beamline Engineer Assistant
KHURSHID
KHURSHID Benazir
PhD Student
PERRIN
PERRIN Jonathan
Beamline Scientist
SCHEEL
SCHEEL Mario
Beamline Scientist
WEITKAMP
WEITKAMP Timm
Beamline Manager

Employment

Click here to access the SOLEIL employment web page 

Technical data

Experimental techniques

Parallel-beam full-field microtomography
- Absorption contrast
- Inline phase contrast
- X-ray grating interferometry (planned)
Nanotomography via full-field zone-plate microscopy (= transmission X-ray microscopy, TXM)
- Absorption contrast
- Zernike phase contrast

Energy range

Microtomography:
- Between 5 and 50 keV (white beam)
- Up to approximately 25 keV (monochromatic)
Nanotomography:
- 10 keV monochromatic (operational)
- Other energies in the range from 5 to 20 keV under test

Beam size at sample

Microtomography:
- From around 0.3 mm × 0.3 mm to 40 mm (H) × 15 mm (V)
Nanotomography:
- Approximately 0.04 mm × 0.04 mm

Beam modes / energy resolution

Microtomography:
- Filtered white beam
- Double crystal monochromator Si-111: ΔE/E = 10-4
- Double multilayer monochromator: ΔE/E = 10-2 (planned 2019)

Nanotomography:
- Double crystal monochromator Si-111: ΔE/E = 10-4

Source

U18 cryogenic in-vacuum undulator

X-ray optics

Entrance aperture: Diaphragm 2.5 mm × 2.0 mm (H×V), 22.7 m from source.
Horizontal "coherence" slit, 23.2 m from source.
Primary slits, 26 m from source.
Double mirror (removable), horizontal reflection, horizontally focusing, f=3.5 m, 35.5 m from source.
Refractive lenses for collimation (removable), 38 m from source (planned).
Secondary horizontal source slit (for use with mirror), 39 m from source.
Double crystal monochromator (Si-111, removable), vertical deflection, 50 m from source.
Double multilayer monochromator (removable), vertical deflection, 53 m from source (planned 2019).

Detectors

All detectors are indirect, lens-coupled systems: the X-ray image is converted into a visible-light image by a scintillator, then projected onto a digital pixel sensor by visible-light lens optics. The effective pixel size is the sensor pixel size divided by the magnification factor of the detector optics.

Detector optics:

Available magnifications: ×1, ×5, ×10, ×20
Other magnification values from ×0.5 to ×50 planned or under test

Sensors:

Model Orca Flash 4.0 V2 pco.4000 Dimax HS4
Manufacturer Hamamatsu PCO PCO
Sensor type CMOS CCD CMOS
Sensor array size 2048×2048 4008×2672 2000×2000
Sensor pixel size 6.5 µm 9.0 µm 11.0 µm
Max. frame rate(a) 20 fps(b) 5 fps 2277 fps(c)
Exposure time per frame 40 µs to 10 s 5 µs to days 1 µs to 40 ms
Frame buffer size ≈1 TB(d) ≈1 TB(d) 36 GB(e)
ADC bit depth 16 bit 14 bit 12 bit
Max. SNR 37000 5500 1600
Peak quantum efficiency 82 % 43 % 47 %
(a)For a full, unbinned frame.
(b)Supplier specifies up to 100 fps but we encounter stability issues above 20 fps.
(c)Not yet fully tested and commissioned.
(d)Limited by hard-disk size of camera PC.
(e)Limited by camera on-board memory.

Scientific opportunities

Information accessible
  • Microstructure and morphology: 2D and 3D distribution of linear attenuation coefficient and/or X-ray refractive index (i.e., electron density)
  • Hidden structures
  • Pore networks (foams…)
  • Fiber networks
  • Subtle density differences
Functional studies
  • Fluid mechanics: percolation, blood flow, etc.
  • Growth processes
  • Failure processes (cracks…)
Application areas
  • Energy
    • Materials for nuclear fusion technology
    • Source rocks
    • Fuel cells
    • Batteries
  • Engineering
    • Hierarchically-structured materials
    • Composites
    • Microstructure of alloys: solidification, dendritic growth
  • Health and biology
    • Cancer: tumor angiogenesis
    • Bone and articular diseases
    • Tissue engineering: scaffolds etc.